ok...this might seem like a really stupid question, but here goes...I want to start messing with the CS. I am currently playing a modded game and I don't want to mess with my mod manager settings. But I want to start learning the CS on Vanilla saves. So here is the dumb question...Can I install the game to a different drive (exterior hard drive) to run vanilla saves and leave my original install on the C: drive without any conflicts? Also, can I run my Vanilla install in windowed mode to have game running while I work in the CS?

Not sure why you would need to have multiple installs. The changes from your mods should show up irrespective of what other mods are active, and even if conflicts do occur, it's often best to become aware of them as you are working instead of beating your head against the wall when it stops working after being moved to your active modded install. If you're concerned about your saved games having some sort of corruption, this is easily solved by having a good clean save or two(mod saved somewhere you aren't committed to a quest or event) which you can load from to test any mods and to no longer rely on the autosaves to preserve your current game progress. When you're testing your mod, load from one of those earlier saves. When not testing your mod (and making sure it isn't active any more) load up from your most recent save. If you notice that there is a good bit of progress between your autosave and your last manual save, just quit the game before loading, disable your mod, load the game, load your autosave, and make a new manual save.

A dual install is possible, but can become rather messy and demand quite alot of storage space a it basically requires flipping back and forth between folder sets.
http://www.tesnexus.com/articles/article.php?id=285